Error: The foot on the back wouldn't connect to the back of the torso normally. I scaffolded it nearly into place, but the connector pegs had to be left off. (I included them in the file in case anyone wants to try inserting them.)

Error: I couldn't get the tubes to flex onto both sets of pegs (perhaps they're not the right length?). For the sake of appearance, they are connected to the pegs on the turbine joints, but if you open the file you will notice that they are not connected to the back pegs.

Window 4741 was available in previous versions of LDD. I hate when a previously available piece is removed!

The Skylights don't really bug me. The bottom pane of glass is slightly inset, but that is the only real issue. If I'm not mistaken, I thought I read that 4737 Corner Convex Ribbed 4X4X6 was in prior versions as well? I could be getting this confused with the Window 4741 though, I only started messing around with LDD 4 weeks ago.

My design philosophy is as long as any substitutions are mainly geometrically correct and look close, it's good enough.

If I'm not mistaken, I thought I read that 4737 Corner Convex Ribbed 4X4X6 was in prior versions as well?

You don't get confused: the brick 4737 was another one available in LDD3 and vanished in LDD4.
My Polaris Lab well knows that
In the LDD4 version (still not inserted here, I have all my sets updated to the last LDD version, but I'm waiting to have decent screenshots ) I had to replace it with a jumble of slope bricks, and the geometry not exactly the same.

Errors:
Missing all prints. 6120 Undercarriage 1X4 (Ski) fails to connect to 4275 Hinge Plate 1X2 1/2 as reported here. The hinges manage to get incredibly close, so for the most part, the model looks fine. No other errors.

The problem about the Plate 4625 and Cockpit 4474 has been reported in the topic of the LDD 4.2.5 bugs?

Yes, as noted in the errors section of the post. The side glass on 4474 Cockpit is slightly too long, causing it to collide with things when placed vertically. To my knowledge, this only affects two official sets, the remaining one is hinged open anyway, so it won't be an issue. So I'd say priority on this bug is rather low.